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Bendixen SM, Jakobsgaard PR, Hansen D, Hejn KH, Terkelsen MK, Bjerre FA, Thulesen AP, Eriksen NG, Hallenborg P, Geng Y, Dam TV, Larsen FT, Wernberg CW, Vijayathurai J, Scott EAH, Marcher AB, Detlefsen S, Grøntved L, Dimke H, Berdeaux R, de Aguiar Vallim TQ, Olinga P, Lauridsen MM, Krag A, Blagoev B, Ravnskjaer K. Single cell-resolved study of advanced murine MASH reveals a homeostatic pericyte signaling module. J Hepatol 2024; 80:467-481. [PMID: 37972658 DOI: 10.1016/j.jhep.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 10/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND & AIMS Metabolic dysfunction-associated steatohepatitis (MASH) is linked to insulin resistance and type 2 diabetes and marked by hepatic inflammation, microvascular dysfunction, and fibrosis, impairing liver function and aggravating metabolic derangements. The liver homeostatic interactions disrupted in MASH are still poorly understood. We aimed to elucidate the plasticity and changing interactions of non-parenchymal cells associated with advanced MASH. METHODS We characterized a diet-induced mouse model of advanced MASH at single-cell resolution and validated findings by assaying chromatin accessibility, bioimaging murine and human livers, and via functional experiments in vivo and in vitro. RESULTS The fibrogenic activation of hepatic stellate cells (HSCs) led to deterioration of a signaling module consisting of the bile acid receptor NR1H4/FXR and HSC-specific GS-protein-coupled receptors (GSPCRs) capable of preserving stellate cell quiescence. Accompanying HSC activation, we further observed the attenuation of HSC Gdf2 expression, and a MASH-associated expansion of a CD207-positive macrophage population likely derived from both incoming monocytes and Kupffer cells. CONCLUSION We conclude that HSC-expressed NR1H4 and GSPCRs of the healthy liver integrate postprandial cues, which sustain HSC quiescence and, through paracrine signals, overall sinusoidal health. Hence HSC activation in MASH not only drives fibrogenesis but may desensitize the hepatic sinusoid to liver homeostatic signals. IMPACT AND IMPLICATIONS Homeostatic interactions between hepatic cell types and their deterioration in metabolic dysfunction-associated steatohepatitis are poorly characterized. In our current single cell-resolved study of advanced murine metabolic dysfunction-associated steatohepatitis, we identified a quiescence-associated hepatic stellate cell-signaling module with potential to preserve normal sinusoid function. As expression levels of its constituents are conserved in the human liver, stimulation of the identified signaling module is a promising therapeutic strategy to restore sinusoid function in chronic liver disease.
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Affiliation(s)
- Sofie M Bendixen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Peter R Jakobsgaard
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Daniel Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Kamilla H Hejn
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Mike K Terkelsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Frederik A Bjerre
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Annemette P Thulesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Niels G Eriksen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Philip Hallenborg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Yana Geng
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Trine V Dam
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Frederik T Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Charlotte W Wernberg
- Department of Gastroenterology and Hepatology, Odense University Hospital, Denmark; Department of Gastroenterology and Hepatology, University Hospital of South Denmark Esbjerg, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Janusa Vijayathurai
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Emma A H Scott
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Ann-Britt Marcher
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, Denmark; Department of Clinical Research, University of Southern Denmark, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Henrik Dimke
- Department of Molecular Medicine, University of Southern Denmark, Denmark; Department of Nephrology, Odense University Hospital, Denmark
| | - Rebecca Berdeaux
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health Houston, USA
| | - Thomas Q de Aguiar Vallim
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, USA; Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, the Netherlands
| | - Mette M Lauridsen
- Department of Gastroenterology and Hepatology, University Hospital of South Denmark Esbjerg, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Odense University Hospital, Denmark; Department of Clinical Research, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark
| | - Kim Ravnskjaer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Center for Functional Genomics and Tissue Plasticity, University of Southern Denmark, Denmark.
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Patikas N, Ansari R, Metzakopian E. Single-cell transcriptomics identifies perturbed molecular pathways in midbrain organoids using α-synuclein triplication Parkinson's disease patient-derived iPSCs. Neurosci Res 2023; 195:13-28. [PMID: 37271312 DOI: 10.1016/j.neures.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
Three-dimensional (3D) brain organoids provide a platform to study brain development, cellular coordination, and disease using human tissue. Here, we generate midbrain dopaminergic (mDA) organoids from induced pluripotent stem cells (iPSC) from healthy and Parkinson's Disease (PD) donors and assess them as a human PD model using single-cell RNAseq. We characterize cell types in our organoid cultures and analyze our model's Dopamine (DA) neurons using cytotoxic and genetic stressors. Our study provides the first in-depth, single-cell analysis of SNCA triplication and shows evidence for molecular dysfunction in oxidative phosphorylation, translation, and ER protein-folding in DA neurons. We perform an in-silico identification of rotenone-sensitive DA neurons and characterization of corresponding transcriptomic profiles associated with synaptic signalling and cholesterol biosynthesis. Finally, we show a novel chimera organoid model from healthy and PD iPSCs allowing the study of DA neurons from different individuals within the same tissue.
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Affiliation(s)
- Nikolaos Patikas
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AH, UK.
| | - Rizwan Ansari
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AH, UK
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AH, UK.
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Li J, Diamante G, Ahn IS, Wijaya D, Wang X, Chang CH, Ha SM, Immadisetty K, Meng H, Nel A, Yang X, Xia T. Determination of the nanoparticle- and cell-specific toxicological mechanisms in 3D liver spheroids using scRNAseq analysis. Nano Today 2022; 47:101652. [PMID: 36911538 PMCID: PMC10004129 DOI: 10.1016/j.nantod.2022.101652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Engineered nanomaterials (ENMs) are commonly used in consumer products, allowing exposure to target organs such as the lung, liver, and skin that could lead to adverse health effects in humans. To better reflect on toxicological effects in liver cells, it is important to consider the contribution of hepatocyte morphology, function, and intercellular interactions in a dynamic 3D microenvironment. Herein, we used a 3D liver spheroid model containing hepatocyte and Kupffer cells (KCs) to study the effects of three different material compositions, namely vanadium pentoxide (V2O5), titanium dioxide (TiO2), or graphene oxide (GO). Additionally, we used single-cell RNA sequencing (scRNAseq) to determine the nanoparticle (NP) and cell-specific toxicological responses. A general finding was that hepatocytes exhibit more variation in gene expression and adaptation of signaling pathways than KCs. TNF-α production tied to the NF-κB pathway was a commonly affected pathway by all NPs while impacts on the metabolic function of hepatocytes were unique to V2O5. V2O5 NPs also showed the largest number of differentially expressed genes in both cell types, many of which are related to pro-inflammatory and apoptotic response pathways. There was also evidence of mitochondrial ROS generation and caspase-1 activation after GO and V2O5 treatment, in association with cytokine production. All considered, this study provides insight into the impact of nanoparticles on gene responses in key liver cell types, providing us with a scRNAseq platform that can be used for high-content screening of nanomaterial impact on the liver, for use in biosafety and biomedical applications.
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Affiliation(s)
- Jiulong Li
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Graciel Diamante
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Darren Wijaya
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Xiang Wang
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Chong Hyun Chang
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Sung-min Ha
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Kavya Immadisetty
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Huan Meng
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - André Nel
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Xia Yang
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Tian Xia
- Center of Environmental Implications of Nanotechnology (UC CEIN), California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
- Division of NanoMedicine, Department of Medicine, California Nanosystems Institute, University of California, Los Angeles, CA 90095, USA
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Nathaniel B, Whiley PAF, Miyamoto Y, Loveland KL. Importins: Diverse roles in male fertility. Semin Cell Dev Biol 2021:S1084-9521(21)00206-8. [PMID: 34426066 DOI: 10.1016/j.semcdb.2021.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023]
Abstract
Regulated nucleocytoplasmic transport is central to the changes in gene expression that underpin cellular development and homeostasis, including in the testis, and proteins in the importin family are the predominant facilitators of cargo transport through the nuclear envelope. Reports documenting cell-specific profiles of importin transcripts and proteins during spermatogenesis led us to hypothesize that importins facilitate developmental switches in the testis. More recently, importins have been shown to serve additional functions, both inside and outside the nucleus; these include acting as subcellular scaffolding, mediating cellular stress responses, and controlling transcription. This paper seeks to provide an overview and update on the functions of importin proteins, with a focus on testis development and spermatogenesis. We present an extended survey of importins by combining published single cell RNAseq data with immunohistochemistry on developing and adult mouse testes. This approach reinforces and broadens knowledge of importins in biological processes, including in spermatogenesis and during testis development, revealing additional avenues for impactful investigations.
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Hesse J, Owenier C, Lautwein T, Zalfen R, Weber JF, Ding Z, Alter C, Lang A, Grandoch M, Gerdes N, Fischer JW, Klau GW, Dieterich C, Köhrer K, Schrader J. Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted murine heart. eLife 2021; 10:e65921. [PMID: 34152268 PMCID: PMC8216715 DOI: 10.7554/elife.65921] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/08/2021] [Indexed: 12/19/2022] Open
Abstract
In the adult heart, the epicardium becomes activated after injury, contributing to cardiac healing by secretion of paracrine factors. Here, we analyzed by single-cell RNA sequencing combined with RNA in situ hybridization and lineage tracing of Wilms tumor protein 1-positive (WT1+) cells, the cellular composition, location, and hierarchy of epicardial stromal cells (EpiSC) in comparison to activated myocardial fibroblasts/stromal cells in infarcted mouse hearts. We identified 11 transcriptionally distinct EpiSC populations, which can be classified into three groups, each containing a cluster of proliferating cells. Two groups expressed cardiac specification markers and sarcomeric proteins suggestive of cardiomyogenic potential. Transcripts of hypoxia-inducible factor (HIF)-1α and HIF-responsive genes were enriched in EpiSC consistent with an epicardial hypoxic niche. Expression of paracrine factors was not limited to WT1+ cells but was a general feature of activated cardiac stromal cells. Our findings provide the cellular framework by which myocardial ischemia may trigger in EpiSC the formation of cardioprotective/regenerative responses.
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Affiliation(s)
- Julia Hesse
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Christoph Owenier
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Tobias Lautwein
- Biologisch-Medizinisches-Forschungszentrum (BMFZ), Genomics & Transcriptomics Laboratory, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Ria Zalfen
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Jonas F Weber
- Algorithmic Bioinformatics, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Zhaoping Ding
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Christina Alter
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Alexander Lang
- Division of Cardiology, Pulmonology and Vascular Medicine, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Maria Grandoch
- Institute of Pharmacology and Clinical Pharmacology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Norbert Gerdes
- Division of Cardiology, Pulmonology and Vascular Medicine, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Jens W Fischer
- Institute of Pharmacology and Clinical Pharmacology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Gunnar W Klau
- Algorithmic Bioinformatics, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital HeidelbergHeidelbergGermany
| | - Karl Köhrer
- Biologisch-Medizinisches-Forschungszentrum (BMFZ), Genomics & Transcriptomics Laboratory, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
| | - Jürgen Schrader
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University DüsseldorfDüsseldorfGermany
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Affiliation(s)
- Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
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